Bottom Line:
We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle.Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization.

Background: Peranakan Ongole (PO) is a major Indonesian Bos indicus breed that derives from animals imported from India in the late 19(th) century. Early imports were followed by hybridization with the Bos javanicus subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight.

Results: We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle. Only two nearly fixed B. javanicus haplotypes were identified, suggesting that most of the B. javanicus variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.

Conclusions: This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle.

Fig3: Estimated phylogenetic tree of cattle breeds. The scale bar represents 10 times the average standard error of the estimated entries in the sample covariance matrix. Migration edges were heat-colored according to the weight of contribution from the parental migrant population. Migration edges show B. javanicus hybridization into PO cattle, and European B. taurus introgression into SGT, BMA and BRM. Vertex a approximates the divergence between Bos primigenius and B. javanicus. Vertex b bifurcates the ancestral B. primigenius into the ancestors of B. taurus and B. indicus. Vertex c is an artificial bifurcation of modern composite breeds SGT and BMA. Vertex d approximates the divergence between European and African B. taurus cattle

Mentions:
Together, these results predicted that the phylogenetic analysis should cluster PO to the B. indicus clade, and a migration edge should be drawn from the B. javanicus branch towards PO. Therefore, we constructed a maximum likelihood tree using TreeMix [10], assuming four migration events representing mixtures in SGT, BMA, BRM and PO. Indeed, the estimated phylogeny behaved as predicted (Fig. 3). As expected, the remaining three estimated migrations were European B. taurus introgressions into SGT, BMA and BRM.Fig. 3

Fig3: Estimated phylogenetic tree of cattle breeds. The scale bar represents 10 times the average standard error of the estimated entries in the sample covariance matrix. Migration edges were heat-colored according to the weight of contribution from the parental migrant population. Migration edges show B. javanicus hybridization into PO cattle, and European B. taurus introgression into SGT, BMA and BRM. Vertex a approximates the divergence between Bos primigenius and B. javanicus. Vertex b bifurcates the ancestral B. primigenius into the ancestors of B. taurus and B. indicus. Vertex c is an artificial bifurcation of modern composite breeds SGT and BMA. Vertex d approximates the divergence between European and African B. taurus cattle

Mentions:
Together, these results predicted that the phylogenetic analysis should cluster PO to the B. indicus clade, and a migration edge should be drawn from the B. javanicus branch towards PO. Therefore, we constructed a maximum likelihood tree using TreeMix [10], assuming four migration events representing mixtures in SGT, BMA, BRM and PO. Indeed, the estimated phylogeny behaved as predicted (Fig. 3). As expected, the remaining three estimated migrations were European B. taurus introgressions into SGT, BMA and BRM.Fig. 3

Bottom Line:
We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle.Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization.

Background: Peranakan Ongole (PO) is a major Indonesian Bos indicus breed that derives from animals imported from India in the late 19(th) century. Early imports were followed by hybridization with the Bos javanicus subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight.

Results: We found that B. javanicus contributes about 6-7% to the average breed composition of PO cattle. Only two nearly fixed B. javanicus haplotypes were identified, suggesting that most of the B. javanicus variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the PLAG1 region on chromosome 14, were found to also affect birth weight in PO cattle.

Conclusions: This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized B. indicus x B. javanicus hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle.